I run a .bat file which executes a command window (system32\cmd.exe) that runs a script to map my employer's network drives (over a VPN) to my home laptop based on my answers to a few questions asked in the script. Anyway this little file used to work fine. Now, for some reason, when I run the batch file the cmd window opens but immediately is stuck on the first question and appears to repeatedly and rapidly blink. Any ideas on what might cause this?

Hard to say - by the 'blinking' I assume you don't just mean the cursor, so can you give more info? The best way to debug a BAT file is to run each command from a prompt and make sure it's working.Just trying to get value-for-money for the $20,000 worth of your products I support...